Evangelion: An Alternate Retelling: True Ending
by Rukaii
Summary: The True End to NGE: An Alternate Retelling that you can find here that I completed in 2006.  The chapters in this story cover the events of the End of Evangelion movie.  S x A
1. Chapter 1

**Neon Genesis Evangelion**

**THE **Alternate Retelling TRUE END

Alpha Chapter

_Darkness had fallen on Tokyo 03... with the defeat of Tabris, NERV had completed it's doctrine of Angel elimination. Shinji, while crestfallen as a result of having to terminate the last Angel, Tabris...or better known as Kaworu to him, understood what needed to be done and accepted it. His feelings aside, he was able to move forward._

_SEELE wasn't done, however, it still yearned for Human Instrumentality. And now, it seemed, that the only obstacle left standing in their way was ironically the very organization to which they've funded thus far in the obligatory 'fight' against the Angels – NERV._

_It was determined that the Japanese Strategic Self Defense Force would be dispatched in order to force the cease and desist of NERV operational procedures and staff. This prompted the "Assault on the Geo Front" to which became a stalemate as NERV refused to adhere to the J.S.S.D.F.'s demands. In response, NERV issued a compulsory order to Shinji and Koji to pilot their Evangelions once again. However, while Koji could be reached... Shinji was unwilling to answer said orders... He was busy visiting Asuka in the hospital where she remained unconscious still..._

"Asuka... did I do the right thing?" Shinji asked aloud as he walked past her bed and put his hand on the wall, "I need to know... Kei and Misato... they tell me I did the right thing. They said that Kaworu wanted to die... so that I should be the existence that should live... I need you Asuka... I need your strength..."

"...baka..."

Shinji's eyes widened upon hearing her voice, he instantly spun around and saw her slowly sitting up in her bed...she turned and looked up at him.

"Asuka... I'm-I'm so glad that you're—"

"Shut up!" Asuka exclaimed, a furious look in her eyes.

"Asuka..."

"...Are you always going to be such a coward? Is acting so pathetic the only thing you can do? You're pitiful!"

"...W-why are you saying things like that? I was so worried about you...we all were...we are."

"You have no idea what happened to me!"

"Actually..."

_Shinji clearly spells out the results of her tests, mixed in with that which Kei had told him during the aftermath after Tabris was defeated... Asuka learned that she wasn't physically assaulted as she was led to believe... _

"...Kei found that out from Ren...huh?"

"Yeah... I... I wanted to tell you. I didn't want you to carry the burden of a false reality... I didn't want you to –"

"...Thanks..." Asuka muttered.

"H-huh?"

"Shut up...I'm not going to repeat myself. So... it's over huh? All the Angels have been defeated. You really did it, Shinji... I won't lie and say that I'm exactly happy that it was you... I wish I could've been the one to do it... but... I guess I do owe you. Despite everything I've said... you're...still here."

"Asuka...it's not exactly over. You see..."

_Shinji explains the current situation to Asuka. Koji was currently in Evangelion Unit 03 dealing with the J.S.S.. Then he handed Asuka a package. It contained her plug suit and A10 nerve chip._

"Shinji, this is probably the best gift you've ever given me." Asuka replied, as she removed all the monitor cables from her body and got out of her bed. She then started to remove her gown...

"A-asuka! W-what are you—"

"I don't mind...but..." Asuka turns her head with a smirk, "If you do look, you're going to have to take responsibility after this is over."

_Shinji gulped and despite the inclination to look, he shut his eyes..._ _to which he suddenly felt something moist touch his lips. Slowly, he opened his eyes..._

"I'm not going to say I'm sorry...for anything I've said before..."

"I...I wouldn't expect you to..."

"Good... alright Shinji... let's go then, Koji's going to need our help."

"Yeah...you're right."

_Asuka and Shinji both exited the hospital room in the medical wing of NERV. Looking around they both noticed that there wasn't signs of anyone around the general vicinity. Pressing onward, they made their way towards the hangar...they needed to get to their Evangelions before it was too late._

_Meanwhile...Evangelion Unit 03 was doing what it could to defend headquarters. At the moment, Koji was managing to hold his own against the rather average military strength of the J.S.S.D.F._

"You're doing good, Koji... just keep it up." Misato said in support.

"I'm doing the best I can... Why are they attacking us? We defeated the Angels... this isn't right."

"To think that our final enemy... would be man itself," Fuyutsuki replied ominously.

_The J.S.S.D.F. were no match for the strength of an Evangelion and it wasn't long before Eva 03 had started to scatter their forces. It was becoming a stalemate..._

"So... they would use the Evangelion... I had hoped to solve this matter peacefully... it seems we're have to fight fire with fire... Drop a succession of N2 mines...we shall see how their defenses hold... then, send in the SEELE elite and mobilize the Eva Series..."

"Acknowledged..."

_The J.S.S.D.F. cleared the area of attack suddenly._

"W-what's going on?" Koji asked with confusion in his voice, "They're...leaving?"

"Shit! They're going to be dropping the bombs! Maximize your AT Field, Koji! As for everyone else – TAKE COVER NOW!"

_Moment later the SEELE blitz ensued, as a plethora of N2 mines were dropped directly on top of NERV HQ... purging a giant hole in the top. Following a force of SEELE Elite para-troopers dropped out of an air convoy that had slipped past Eva 03's defense net. Unable to intercept them, Koji could only watch as the base was infiltrated by SEELE operatives en mass. It proved to be irrelevant, however, as he also noticed a flocking swarm circling the skies from the outside perimeter... the Eva Series..._

"Koji, you need to stand your ground – help will be there shortly!"

"R-right..."

"Dammit, where's Shinji! I need him to sortie on the double!" Misato shouted.

"Camera's have just picked up Shinji's location – he's with Asuka! They're leaving the medical wing now!"

"But... that area's completely cut off from the rest of the base due to the N2 mines – the SEELE para troopers have entered the base at that junction!" Koji shouted.

"...Looks like it's time to go maverick again..." Misato muttered as she cocked her handgun.

"Fuyutsuki... take care of this base." Gendo Ikari stated cryptically, "There's a matter to which I need to resolve."

"Give my regards to Yui." Were Fuyutsuki's last words to Gendo before he had lowered out of sight using his own private lift that descended deep into terminal dogma...

"Vice Commander? Where's the Commander headed?" Misato questioned.

"It's not a matter to which concerns you, Major. For the time being, however, are you going?"

"Yes, I need to ensure that those kids make it to their Evas."

"Good... I'll take care of things here. Good luck, Major."

"Thank you..."

_Misato bolted down the hall outside the control center. She was outside of the only 'safe' zone of headquarters now. As she progressed downward the hallway, opposition appeared from around the corner. Taking action, Misato shot two quick shots towards them, downing them. She continued onward..._

_Meanwhile...Shinji and Asuka were running down a darkened corridor. The section of the base they were in had lost most primary power with only occasional flickers of light to guide their way...When they rounded the corner... a group of armed SEELE soldiers stood, arms aimed at them..._

"Nothing personal kids...but this is the end of the road."

_Then, dropping in from behind from the vents below was Ren who wasted no time attacking the soldiers. She sliced the head clean off the first on her left, and then stabbed the second through the back and out the stomach... leaving only one out of the three that made up this group of soldiers..._

"Y-you bitch... Die!"

"You first..." Ren retorted stabbing the soldier through his throat before he could pull the trigger. He slumped to the ground, feverishly trying to prevent his jugular from squirting out blood but to no avail... with each beat of his heart he bleed outward and died...

"You!" Asuka shouted with fury in her eyes.

"Relax, Asuka... she's not here to harm us... she's here to help."

"Kei? Is that true?"

"Yes, she has no reason to stay tied with SEELE... so for the time being, she is aiding us against SEELE. There's nothing like a grand counter attack to get back at your enemy on the defensive."

"We need to get moving."

"Right. We're almost at the hangar. Stay close to us and we'll get you there safely."

"Kei..." Shinji started to say.

"Save it kid, we've got no time for chit-chat."

"..." Nodding in understanding, Shinji followed Asuka who in turn followed Kei towards the hangar. Ren brought up the rear guard position as they advanced...

**Author's Comments**

_Well it's been 4 years coming since I've returned to working on the story that put me on the Fan-Fiction map... well that might be tooting my own horn to a bit of a stretch, but be it as it may, facts are facts and it has been indeed almost 4 years since I have updated this story. Those of you who haven't drawn the correlations to my original work "Neon Genesis Evangelion: An Alternate Retelling" should know now that this is infact the TRUE END that I had promised those 4 years ago._

_This is the first part of what is probably going to be a three or four part story. It won't be very long, as it's the ending scenario to my alternate retelling account of Evangelion. Due to various reasons this will be a bit more straight forward and probably a bit less psychological than the events happening during the bulk of the 25 chapters of the story but that's because I'm working to tie up the loose ends and try to bring a better understanding to why certain characters do what they're doing. And of course, there's the big question of what will happen next with the potential of Third Impact on the horizon. I want you all to understand ahead of time that my frame of mind is a lot different than it was four years ago given a lot of various events that have happened in my personal life since then. So, while I won't spoil anything, expect a straightforward in-your-face approach to the 'fates' of our characters. I can't promise everyone will make it out of this alive, but what I can promise is that I'm going to do everything I can to make this TRUE END something to live up to the four years I have been away from this project._

_Thank you for all those who have favored this story well long after I had written it and thank you for those who read this even after I have waited so long to begin the wrap up work on it's completion. Look forward to the next part -Beta Chapter- next weekend. Thank you again, and I hope you enjoyed the contents of Alpha Chapter._

_-**Rukaii** _


	2. Chapter 2

**Neon Genesis Evangelion**

**THE **Alternate Retelling TRUE END

Beta Chapter

_Descending into the depths of NERV, Commander Gendo Ikari had arrived at the deepest level – Terminal Dogma. In front of him stood Rei Ayanami._

"Rei... It's time."

"..."

"Rei—"

Gendo had started to say as he reached his hand outward towards Rei...however...

"No!" Rei suddenly shouted with emotion in her voice. Simultaneously, an AT Field resonated around her body which grabbed, twisted, and shattered Gendo's arm like that of a twig. The sick blood curdling sounds which followed as Gendo's hand was absolutely obliterated into a mass of thick, murky red and white matter...

"Gah..." Gendo grunted in pain as he retracted his arm – what was left of it – holding it close to his torso, "Rei...Why?"

"Because... I am not yours to control... I am the last...There were those before me who may have listened to you without a second thought. There were those before me who would've died for you without a second thought. I... am not like them. I have a conscious which expands far and beyond that of a single vessel. I am no mere container-no vessel for your 'desire's'... I AM Rei Ayanami."

"...I see..." Gendo lets his mangled arm down and adjusts his glasses with his good hand, "...Then our existence is indeed doomed..."

"You're merely delusional, Commander Ikari... What you want is to return to Yui. That is, in essence, what SEELE wants. They desire human instrumentality. You implanted Adam into your hand, thus assimilating yourself to Adam... If you assimilate Adam into my being... there is of no doubt that Third Impact will inevitably occur...Third Impact will be the finality of mankind as we are now... To that end... I shall not allow you to place Adam inside me. I will not be the vessel of Adam nor the vessel of Yui or anyone for that matter... I am Rei Ayanami, I live, therefore I am... my own soul. Neither you, nor SEELE, nor anyone can take from me my existence." Rei declares pointing at Gendo, "I will live in this world, with these people... Human Instrumentality... Third Impact... will never happen. Yui is dead, Commander Ikari... you need to accept that."

"...I already have...it seems that in my inability to love myself has only caused trouble for those around me after her death... even Shinji... I suppose this is an acceptable fate... Rei... If you won't allow me to return to Yui through you...then..."

"You needed ask... I will grant that final request..."

_All remained still in terminal dogma...amidst the pool of LCL which surrounded the platform on which they stood... in the moments following, blood would rain down and pour into the LCL pool..._

_Meanwhile...running down a corridor within NERV headquarters, Kei and Ren led the way with Shinji and Asuka in tow. Suddenly, gun fire opened up from the SEELE special soldiers whom had infiltrated. Deflecting an array of bullets with his katana, Kei then removed an Uzi from behind his back belt and opened fire, taking down one of the guards. In following, they dove into the near by corridor to their left to duck and cover from the onslaught of bullets being shot their way..._

"There's only a few guards left in that group... what should we do?" Asuka asked.

"...We're not exactly equipped to fend them all off at once... and not to mention I'm out of bullets," Kei assessed, throwing his Uzi 9mm to the floor beside him.

"...We will have to create a diversion," Ren added, standing up as she brandished her katana.

"But...if you rush out there...you'll die..." Shinji replied with concern.

"...And if I do nothing, we all die. They won't wait long, once they realize we are out of a means to fight back...they will storm down here and shoot us dead."

"Ren's right..." Kei interjected, as he slowly pulled himself to his feet, wincing.

"Y-you're hurt!" Asuka exclaimed.

"...It's just a scratch, nothing too bad... I've been hurt worse before...Now... we have to get you two to your Eva's... So..."

_Before Kei could finish his sentence, the sound of shots could be heard in the distance. The confused state of the SEELE soldiers could be understood from their scattered shouting._

_Misato ran down the hall firing rounds from her handgun. The first shot pierced the first soldiers helmet and into his brain case – killing him instantly. Her second shot hit it's mark too, through and through the second soldier's neck. He fell down and bleed out. The final soldier was hit with a high kick as Misato jumped through the air avoiding his panicked flurry shooting, slammed him against the metal corridor walls and shot him upward through his jaw up into his brain..._

"Misato...?"

"We don't have a lot of time. The entire base is overrun. We have to get the children to their Eva's." Misato replied with much composure.

"...Yes, you're right." Kei answered.

_Area 667 in NERV was the last section they had to navigate before they could hope to get Asuka and Shinji to the elevator that would take them to their Evangelions. This also happened to be the zone where SEELE had placed the bulk of it's special soldiers. Even more so, all throughout NERV, these SEELE specials were eliminating every NERV personnel they came into contact with. There was no mercy shown for even those that raised their arms in surrender. It was clear that SEELE had no plans to leave NERV to it's own devices any longer. NERV lifeline had been pulled and SEELE would see that it was terminated before the night fell... that was it's agenda..._

_Ren stood up, taking a few steps away from the others as she scoped the surroundings... below, there was a graveyard of all the failed Evangelion units that preceded Unit 00. She turned back towards the others, her back to the railing that separated her from the Eva graveyard below..._

"This is where it all began. This was the original control center of Gehirn. Before the inception of NERV... this was the base of operations. The original birthplace of the Evangelion. Despite the numerous failings, this is where your Eva 01, Shinji, was born..."

"Born?"

"Yes, by now you have realized that each Evangelion possesses a soul. It is, after all, a living entity. The armor it wears is merely a shackle to keep the true BEAST at bay. However, with a capable pilot, the necessity for such shackling becomes irrelevant."

"The Eva is...alive?" Asuka muttered, "So...wonder girl had a point after all..."

"Enough of this we have too—" Ren stopped in mid-sentence, and then slowly placed her hand on her chest. The crimson color began to seep into her clothing. She staggered backwards, her eyes wide with shock.

"H-how...I...have the gift...to die...like this... It wasn't...supposed to be..."

"You misunderstand the true meaning of the **Gift**, Ren!" A voice shouted from the below, amidst the graveyard of Evangelions...

"Ritsuko?" Misato exclaimed.

"Ren!" Kei bolted to his feet towards Ren, however, he was too late. Ren's body fell over the railing, falling over 200 feet to the ground below. Where it hit with a sickening, blood curdling, bone breaking sound... to which all movement and life for that matter ceased...

_Ritsuko lowered her rifle and set it between her legs. She sat on the remains of one of the failed Eva units, she brushed back her now natural dark brown hair and flicked a cigarette from her hand to the ground._

"How did you get out of the isolation ward?"

"Oh Misato... it was easy. SEELE let me out."

"SEELE... that name again..." Misato muttered, "So... you're in league with them, then?"

"Shouldn't that be a natural reasoning by this point, Misato? I don't really care what you do now. Send those children to their Eva's for all I care. My mission here is done."

"You bitch... why Ren? Why did you kill her!" Kei exclaimed, slamming his hands on the railing.

"Kurosawa... it's elementary really, Ren had planned to turn against SEELE.. and SEELE can't have it's own turning against them now can they? They contacted me while I was in the isolation ward and gave me an ultimatum – If I wanted to continue to live and see the outcome of Human Instrumentality... then, I would have to eliminate a certain traitor. That traitor was Ren. Well... now that that's out of the way. I suppose this is goodbye. And Misato, my dear _friend_, do take care. It would be a _shame_ if you were unable to live to see the new future of mankind..."

_Leaving the rifle where it was at, Ritsuko stood up and threw her lab coat over her shoulder and proceeded to simply walk away._

"Ritsuko!" Misato shouted, aiming her gun at her from above.

"...What are you going to shoot me? You do know that Ren was the one who killed Kaji, right?"

"W-what?"

_Misato could no longer hold her gun steady, to which she eventually lowered it entirely..._

"I knew you'd understand... Good bye, Misato."

_And those were the last words Misato would hear from Ritsuko...before Ritsuko would vanish into the darkness and out of sight..._

_In silence, Misato and Kei walked slowly towards the far end of the walkway. Shinji and Asuka followed in silence as well..._

_Outside, the 9 Evangelion Units which comprised the rest of the Eva Series had completed circling around Evangelion Unit 03. In succession, they would land, each then would retract it's vulture like wings into it's back. The white framed units each possessed a rather uncanny and unsettling smile, like that of a joker._

"Koji, can you hear me? It's Misato."

"Yeah I can hear you."

"I heard from Maya... they rolled out the rest of the Eva Series... We still have to get Shinji and Asuka to their Eva's...so...for the time being, you're just going to have to go it alone – be careful – don't die out there..."

"Okay..."

_Koji swallowed and then took a deep breath..._

"All my life... I've always depended on others to bail me out of trouble. I was always so afraid, and scared. I've always held back in my potential in whatever I did... but... I don't want to be afraid anymore. I want to be useful. I want to help my friends...my family...my comrades...Mother...Father...Misato...Kei-aniki...Shinji-aniki...Rei-neesan...and...especially Asuka oneechan...They're all depending on me... I cannot let them down. I won't let them down, because - I am Koji Misawa - pilot of Evangelion unit 3! I will fight with courage!I won't be afraid anymore! I'm going to give it all I got! Please, Mother, lend me your strength!"

_In that instant, Koji Misawa's synchro ratio began to rise exponentially. For the first time, Koji was truly mentally prepared to fight...however, in truth, the fight that which lay ahead of him was a daunting one to which no one could ever be truly and fully prepared to enter... Will Koji be able to fend off the 9 – to – 1 odds to which he faces? Will Asuka and Shinji make it to their Eva's in time? Or will SEELE special soldiers prevent Misato and Kei from safeguarding them there? Will Kei's injuries play a factor in this? What is Gendo's fate? What will Rei Ayanami do now that she has for the first time realized her true desires? All the answers lie ahead...in the shadows... until next time..._

**Author's Comments**

_Well there's the 2nd installment of the True End. I'm sure you've got questions. Some of which I hope will be answered in the final few installments that are yet to come. I'm glad I was able to get this up in the time frame I allotted – to be honest, I almost didn't get to work on it due to my very hectic work schedule this week. But I managed to find time and get to work. I'm aware that I've got other unfinished projects here on FF, but, this one is my top priority as it stands. It's been four years in the making, it's time it gets completed. Once again, thanks for reading._

_~Rukaii_


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